ZBTB38
Basic information
Region (hg38): 3:141324213-141449792
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (103 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB38 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001376113.1. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | |||||
missense | 96 | 105 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 96 | 8 | 4 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZBTB38 | protein_coding | protein_coding | ENST00000514251 | 1 | 125580 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.999 | 0.000509 | 124756 | 0 | 5 | 124761 | 0.0000200 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.31 | 494 | 661 | 0.747 | 0.0000364 | 7956 |
Missense in Polyphen | 125 | 264.46 | 0.47267 | 3243 | ||
Synonymous | 1.52 | 227 | 258 | 0.879 | 0.0000161 | 2260 |
Loss of Function | 5.02 | 3 | 35.1 | 0.0856 | 0.00000195 | 468 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.0000995 | 0.0000993 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000265 | 0.0000265 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl- CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA- replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity). {ECO:0000250|UniProtKB:Q5EXX3, ECO:0000269|PubMed:16354688, ECO:0000269|PubMed:24726359}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.0810
- rvis_EVS
- 0.03
- rvis_percentile_EVS
- 55.81
Haploinsufficiency Scores
- pHI
- 0.476
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.806
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zbtb38
- Phenotype
Gene ontology
- Biological process
- regulation of DNA replication;regulation of transcription, DNA-templated;cellular response to DNA damage stimulus;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;chromosome;blood microparticle
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;methyl-CpG binding;protein homodimerization activity;metal ion binding